{
  "_id": "6a103398acfb0bcc41c98637",
  "Package": "corncob",
  "Title": "Count Regression for Correlated Observations with the\nBeta-Binomial",
  "Version": "0.4.3",
  "Authors@R": "c(\nperson(\"Bryan D\", \"Martin\", role = \"aut\"),\nperson(\"Daniela\", \"Witten\", role = \"aut\"),\nperson(\"Sarah\", \"Teichman\", role = \"ctb\"),\nperson(\"Amy D\", \"Willis\", email = \"adwillis@uw.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Thomas W\", \"Yee\", role = \"ctb\", comment = \"VGAM library\"),\nperson(\"Xiangjie\", \"Xue\", role = \"ctb\", comment = \"VGAM library\")\n)",
  "Description": "Statistical modeling for correlated count data using the\nbeta-binomial distribution, described in Martin et al. (2020)\n<doi:10.1214/19-AOAS1283>. It allows for both mean and\noverdispersion covariates.",
  "URL": "https://github.com/statdivlab/corncob,\nhttps://statdivlab.github.io/corncob/",
  "BugReports": "https://github.com/statdivlab/corncob/issues",
  "License": "GPL (>= 2)",
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  "VignetteBuilder": "knitr",
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  "Repository": "https://statdivlab.r-universe.dev",
  "Date/Publication": "2025-11-13 18:19:04 UTC",
  "RemoteUrl": "https://github.com/statdivlab/corncob",
  "RemoteRef": "HEAD",
  "RemoteSha": "d7ac4c8a3f757eef6c7d8006431494528ead8e92",
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  "Packaged": {
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    "User": "root"
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  "Author": "Bryan D Martin [aut],\nDaniela Witten [aut],\nSarah Teichman [ctb],\nAmy D Willis [aut, cre],\nThomas W Yee [ctb] (VGAM library),\nXiangjie Xue [ctb] (VGAM library)",
  "Maintainer": "Amy D Willis <adwillis@uw.edu>",
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  "_user": "statdivlab",
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  "_published": "2026-05-22T10:44:40.076Z",
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  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/statdivlab/corncob",
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    "author": "Sarah Teichman <teichs@uw.edu>",
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    "message": "Merge pull request #190 from luhann/tse\n\nAdd full SummarizedExperiment support",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.json",
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    "extra/readme.html",
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      "date": "2021-03-11"
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    },
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    "bbdml",
    "checkNested",
    "clean_taxa_names",
    "clean_taxa_names_se",
    "contrastsTest",
    "convert_phylo",
    "convert_sumexp",
    "coth",
    "differentialTest",
    "fishZ",
    "genInits",
    "HDIbetabinom",
    "hessian",
    "invfishZ",
    "invlogit",
    "logit",
    "lrtest",
    "otu_to_taxonomy",
    "otu_to_taxonomy_se",
    "pbLRT",
    "pbRao",
    "pbWald",
    "qbetabinom",
    "raotest",
    "sand_vcov",
    "sandSE",
    "score",
    "waldchisq",
    "waldt",
    "warn_phyloseq",
    "warn_sumexp"
  ],
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      "name": "ibd_phylo_otu",
      "title": "IBD data, OTU count data frame.",
      "object": "ibd_phylo_otu",
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      ],
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      ],
      "rows": 36349,
      "table": true,
      "tojson": true
    },
    {
      "name": "ibd_phylo_sample",
      "title": "IBD data, sample data frame.",
      "object": "ibd_phylo_sample",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample",
        "gender",
        "age",
        "DiseaseState",
        "steroids",
        "imsp",
        "abx",
        "mesalamine",
        "ibd",
        "activity",
        "active",
        "race",
        "fhx",
        "imspLEVEL",
        "SampleType"
      ],
      "rows": 91,
      "table": true,
      "tojson": true
    },
    {
      "name": "ibd_phylo_taxa",
      "title": "IBD data, taxonomy data frame.",
      "object": "ibd_phylo_taxa",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Kingdom",
        "Phylum",
        "Class",
        "Order",
        "Family",
        "Genus",
        "Species"
      ],
      "rows": 36349,
      "table": true,
      "tojson": true
    },
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      "name": "soil_phylo_otu",
      "title": "Soil data, otu table as data frame.",
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      "table": true,
      "tojson": true
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      "name": "soil_phylo_taxa",
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      "object": "soil_phylo_taxa",
      "class": [
        "matrix",
        "array"
      ],
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        "Phylum",
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        "Order",
        "Family",
        "Genus",
        "Species"
      ],
      "rows": 7770,
      "table": true,
      "tojson": true
    },
    {
      "name": "soil_phylum_contrasts_otu",
      "title": "Small soil phylum data for contrasts examples, otu table as data frame",
      "object": "soil_phylum_contrasts_otu",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "S204",
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        "S247",
        "S012",
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      "rows": 39,
      "table": true,
      "tojson": true
    },
    {
      "name": "soil_phylum_contrasts_sample",
      "title": "Small soil phylum data for contrasts examples, sample data as data frame",
      "object": "soil_phylum_contrasts_sample",
      "class": [
        "data.frame"
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      "fields": [
        "Plants",
        "DayAmdmt",
        "Amdmt",
        "ID",
        "Day"
      ],
      "rows": 56,
      "table": true,
      "tojson": true
    },
    {
      "name": "soil_phylum_small_otu",
      "title": "Small soil phylum data for examples, otu table as data frame",
      "object": "soil_phylum_small_otu",
      "class": [
        "data.frame"
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      "fields": [
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        "S222",
        "S239"
      ],
      "rows": 39,
      "table": true,
      "tojson": true
    },
    {
      "name": "soil_phylum_small_otu1",
      "title": "Small soil phylum data for examples, sample data as data frame combined with counts for OTU 1 and sequencing depth.",
      "object": "soil_phylum_small_otu1",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Plants",
        "DayAmdmt",
        "Amdmt",
        "ID",
        "Day",
        "W",
        "M"
      ],
      "rows": 32,
      "table": true,
      "tojson": true
    },
    {
      "name": "soil_phylum_small_sample",
      "title": "Small soil phylum data for examples, sample data as data frame",
      "object": "soil_phylum_small_sample",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Plants",
        "DayAmdmt",
        "Amdmt",
        "ID",
        "Day"
      ],
      "rows": 32,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "corncob-package",
      "title": "Corncob package documentation.",
      "topics": [
        "corncob-package",
        "corncob"
      ]
    },
    {
      "page": "bbdml",
      "title": "Maximum Likelihood for the Beta-binomial Distribution",
      "topics": [
        "bbdml"
      ]
    },
    {
      "page": "checkNested",
      "title": "Check for nested models",
      "topics": [
        "checkNested"
      ]
    },
    {
      "page": "clean_taxa_names",
      "title": "Rename taxa",
      "topics": [
        "clean_taxa_names"
      ]
    },
    {
      "page": "clean_taxa_names_se",
      "title": "Rename taxa",
      "topics": [
        "clean_taxa_names_se"
      ]
    },
    {
      "page": "contrastsTest",
      "title": "Identify differentially-abundant and differentially-variable taxa using contrasts",
      "topics": [
        "contrastsTest"
      ]
    },
    {
      "page": "convert_phylo",
      "title": "Function to subset and convert phyloseq data",
      "topics": [
        "convert_phylo"
      ]
    },
    {
      "page": "convert_sumexp",
      "title": "Function to subset and convert SummarizedExperiment data",
      "topics": [
        "convert_sumexp"
      ]
    },
    {
      "page": "coth",
      "title": "Hyperbolic cotangent transformation",
      "topics": [
        "coth"
      ]
    },
    {
      "page": "dbetabin",
      "title": "Betabinomial density",
      "topics": [
        "dbetabin"
      ]
    },
    {
      "page": "dbetabin_neg",
      "title": "Negative betabinomial density",
      "topics": [
        "dbetabin_neg"
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    },
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